To compare fixation deviation and stability with soft contact lens correction and device built-in auto-focus system during optical coherence tomography angiography (OCTA). This observational study measured OCTA metrics first with contact lens correction, followed by removal of contact lenses, using the device auto-focus system at a University Optometry Clinic, Hong Kong. All participants were habitual soft contact lens wearers with either low or high myopia. OCTA measurements were obtained using a spectral domain OCTA. Fixation deviation was distance (in pixels) of the fovea to the center of the OCTA measurement grid. Fixation stability was test–retest repeatability (TRR) and coefficient of variation (CV) of fixation deviation from three consecutive OCTA measurements. OCTA metrics included vessel length density (VD), perfusion density (PD), and foveal avascular zone (FAZ) area. Averaged OCTA metrics were calculated from three measurements and compared between the two correction methods. The mean ± SD spherical equivalent of 74 eyes from 74 myopes measured was − 1.94D ± 0.75D in low myopes (n = 37) and − 7.97D ± 1.31D in high myopes (n = 37). When corrected with contact lenses, visual acuities of high myopes (median [IQR], − 0.06 [0.08] logMAR) and low myopes (− 0.02 ± 0.08 logMAR) were similar (P = 0.060), and with similar fixation deviation (5.0 ± 2.2 pixels vs 5.3 [3.6] pixels; P = 0.689). High myopes had poorer fixation stability than low myopes (TRR: 10.2 pixels vs 7.5 pixels; CV: 65% vs 54%, respectively). The worst fixation stability occurred when high myopes were corrected using the auto-focus system (TRR: 12.5 pixels, CV: 72%). The difference in VD and PD was within 1 mm−1 and 1%, respectively. The FAZ area was similar. Difference in OCTA metrics was small in each refractive group (< 1 mm−1 in VD, and < 2% in PD). High myopes had more stable fixation when corrected when wearing contact lenses. Subjects with good contact lens corrected visual acuity should wear their contact lenses during OCTA measurements.